rs1053578

chr17-45143918-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135705.3(ACBD4):c.*347T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 301,424 control chromosomes in the GnomAD database, including 547 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.047 (231 hom., cov: 32)
  • Exomes 𝑓: 0.060 (316 hom.)
• Consequence: ACBD4 NM_001135705.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

ACBD4 (HGNC:23337): (acyl-CoA binding domain containing 4) This gene encodes a member of the acyl-coenzyme A binding domain containing protein family. All family members contain the conserved acyl-Coenzyme A binding domain, which binds acyl-CoA thiol esters. They are thought to play roles in acyl-CoA dependent lipid metabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACBD4	NM_001135705.3	c.*347T>C		3_prime_UTR_variant	10/10	ENST00000321854.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACBD4	ENST00000321854.13	c.*347T>C		3_prime_UTR_variant	10/10	1	NM_001135705.3	P1

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7173 AN: 151954 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0628

GnomAD4 exome AF: 0.0600 AC: 8954 AN: 149352 Hom.: 316 Cov.: 0 AF XY: 0.0614 AC XY: 4789 AN XY: 77986

Gnomad4 AFR exome AF: 0.0107

Gnomad4 AMR exome AF: 0.0410

Gnomad4 ASJ exome AF: 0.0876

Gnomad4 EAS exome AF: 0.000105

Gnomad4 SAS exome AF: 0.0696

Gnomad4 FIN exome AF: 0.0313

Gnomad4 NFE exome AF: 0.0687

Gnomad4 OTH exome AF: 0.0590

GnomAD4 genome AF: 0.0471 AC: 7169 AN: 152072 Hom.: 231 Cov.: 32 AF XY: 0.0455 AC XY: 3383 AN XY: 74364

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.0292

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0607 Hom.: 29

Bravo AF: 0.0448

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	8.2
Dann	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1053578; hg19: chr17-43221285;